Application of Bioinformatics in Search for Cleavable Peptides of SARSCoV Mpro and Chemical Modification of Octapeptides

Qishi      Du; Shuqing      Wang; Zhiqin      Jiang; Weina      Gao; Yun      Li; Dongqing      Wei; Kuo-Chen      Chou

doi:10.2174/1573406053765468

Abstract

According to the “distorted key” theory as elaborated in a review article years ago (Chou, K.C.: Analytical Biochemistry, 1996, 233, 1-14), the knowledge of the cleavable peptides by SARS-CoV Mpro (severe acute respiratory syndrome coronavirus main proteinase) can provide very useful insights on developing drugs against SARS. In view of this, the softwares, ZCURVE_CoV 1.0 and ZCURVE_CoV 2.0 (http: / / tubic.tju.edu.cn / sars / ), developed recently for SARS-Coronavirus are used to analyze the 36 complete SARS-Coronavirus RNA sequences in the gene bank NCBI (http: / / www.ncbi.nlm.nih.gov / ) from different sources for protein coding genes, and to search for the cleavage sites of SARS-CoV Mpro in polyproteins pp1a and pp1ab. A total of 396 cleavage points are found in the 36 SARS-Coronavirus and 11 cleavable octapeptides abstracted from the 396 cleavage sites. The statistical distributions of amino acids for the cleavable octapeptides at the subsites R4, R3, R2, R1, R1, R2, R3 and R4 are calculated. The cleavage-specific positions are on R2, R1 and R1, and the positions R3 and R4 are featured by some certain specificity for SARS-CoV Mpro. The structural characters of amino acid residues around the cleavage-specific positions are discussed. Two most promising octapeptides, i.e., NH2-ATLQ↓AIAS-COOH and NH2-ATLQ↓AENV-COOH, are selected to be the candidates for chemical modification, converting into the inhibitors of SARS-CoV Mpro. A possible strategy to convert a cleavable octapeptide by SARS enzyme into a drug candidate against SARS is elucidated.

Keywords: sars, coronavirus, gene identification, sars-cov mpro, octapeptide, peptide bond modification, Inhibitor, distorted key theory